[English] 日本語
Yorodumi- EMDB-25033: T-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25033 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | T-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with OCP - local refinement | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Function / homology | Function and homology information light absorption / Lyases / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity / photosynthesis / lyase activity Similarity search - Function | |||||||||
Biological species | Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) / Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Sauer PV / Sutter M / Dominguez-Martin MA / Kirst H / Kerfeld CA | |||||||||
Funding support | European Union, 1 items
| |||||||||
Citation | Journal: Nature / Year: 2022 Title: Structures of a phycobilisome in light-harvesting and photoprotected states. Authors: María Agustina Domínguez-Martín / Paul V Sauer / Henning Kirst / Markus Sutter / David Bína / Basil J Greber / Eva Nogales / Tomáš Polívka / Cheryl A Kerfeld / Abstract: Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded ...Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching. Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystis sp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP-PBS complex, quenching is achieved through the binding of four 34 kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60 Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties, we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_25033.map.gz | 88.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-25033-v30.xml emd-25033.xml | 23.7 KB 23.7 KB | Display Display | EMDB header |
Images | emd_25033.png | 185.1 KB | ||
Masks | emd_25033_msk_1.map | 178 MB | Mask map | |
Others | emd_25033_half_map_1.map.gz emd_25033_half_map_2.map.gz | 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25033 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25033 | HTTPS FTP |
-Validation report
Summary document | emd_25033_validation.pdf.gz | 825.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_25033_full_validation.pdf.gz | 825.2 KB | Display | |
Data in XML | emd_25033_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | emd_25033_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25033 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25033 | HTTPS FTP |
-Related structure data
Related structure data | 7sccMC 7sc7C 7sc8C 7sc9C 7scaC 7scbC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_25033.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_25033_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_25033_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_25033_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Complex of phycobilisome from Synechocystis PCC 6803 with OCP
Entire | Name: Complex of phycobilisome from Synechocystis PCC 6803 with OCP |
---|---|
Components |
|
-Supramolecule #1: Complex of phycobilisome from Synechocystis PCC 6803 with OCP
Supramolecule | Name: Complex of phycobilisome from Synechocystis PCC 6803 with OCP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
---|---|
Source (natural) | Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) |
-Macromolecule #1: Allophycocyanin alpha chain
Macromolecule | Name: Allophycocyanin alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 / Kazusa |
Molecular weight | Theoretical: 17.429807 KDa |
Sequence | String: MSIVTKSIVN ADAEARYLSP GELDRIKAFV TGGAARLRIA ETLTGSRETI VKQAGDRLFQ KRPDIVSPGG NAYGEEMTAT CLRDMDYYL RLVTYGVVSG DVTPIEEIGL VGVREMYRSL GTPIEAVAQS VREMKEVASG LMSSDDAAEA SAYFDFVIGK M S |
-Macromolecule #2: Allophycocyanin beta chain
Macromolecule | Name: Allophycocyanin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 / Kazusa |
Molecular weight | Theoretical: 17.231604 KDa |
Sequence | String: MQDAITAVIN SADVQGKYLD GAAMDKLKSY FASGELRVRA ASVISANAAT IVKEAVAKSL LYSDVTRPGG NMYTTRRYAA CIRDLDYYL RYATYAMLAG DASILDERVL NGLKETYNSL GVPISSTVQA IQAIKEVTAS LVGADAGKEM GVYLDYICSG L S |
-Macromolecule #3: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...
Macromolecule | Name: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 / Kazusa |
Molecular weight | Theoretical: 7.817174 KDa |
Sequence | String: MRMFRITACV PSQTRIRTQR ELQNTYFTKL VPYDNWFREQ QRIMKMGGKI VKVELATGRP GTNAGLA |
-Macromolecule #4: Phycobiliprotein ApcE
Macromolecule | Name: Phycobiliprotein ApcE / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: Lyases |
---|---|
Source (natural) | Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 / Kazusa |
Molecular weight | Theoretical: 100.412703 KDa |
Sequence | String: MSVKASGGSS LARPQLYQTV PVSAISQAEQ QDRFLEGSEL NELTAYFQSG ALRLEIAETL TQNADLIVSR AANRIFTGGS PLSYLEKPV ERQPALVGAS SDSRNGSVTY AESNGSGGLF GGLRSVFSST GPIPPGFRPI NIARYGPSNM QKSLRDMSWF L RYTTYAIV ...String: MSVKASGGSS LARPQLYQTV PVSAISQAEQ QDRFLEGSEL NELTAYFQSG ALRLEIAETL TQNADLIVSR AANRIFTGGS PLSYLEKPV ERQPALVGAS SDSRNGSVTY AESNGSGGLF GGLRSVFSST GPIPPGFRPI NIARYGPSNM QKSLRDMSWF L RYTTYAIV AGDPNIIVVN TRGLKEVIEN ACSIDATIVA IQEMRAASAD YFRNNAQAKE IVLQYFDILL SEFKAPTPAN KV RQGPSND IQGLELPQSY FNAAAKRQKY AMKPGLSALE KNAVIKAAYR QIFERDITKA YSQSISYLES QVRNGDISMK EFV RRLAKS PLYRKQFFEP FINSRALELA FRHILGRGPS SREEVQKYFS IVSSGGLPAL VDALVDSQEY ADYFGEETVP YLRG LGVEA QECRNWGMQQ DLFSYSAPFR KVPQFITTFA QYDRPLPDQH VYGSGNDPLE IQFGAIFPKE TRNPSKRPAP FNKDT KRIL IHRGPAVNNQ VGNPSAVGEF PGSLGAKVFR LNGGLPGAKV GKNTGTSVKF GESSTQALIR AAYRQVFGRD LYEGQR LSV AEIQLENGDI SVREFIKRLA KSELFLKLYW APHYVCKAIE YMHRRLLGRP TYGRQEMNQY FDIASKQGFY AVVEAMI DS KEYSDAFGED TVPYERYLTP GGLQMRSARV GSLREDIGQR VDKEVTPRFV ELGQVSAIRT EPEIAYRSNQ GVTRQRQQ T KVFKLVSTYD KVAVKNAIRA AYRQVFERDL EPYIINSEFT ALESKLSNNE INVKEFIEGL GTSELYMKEF YAPYPNTKV IEMGTKHFLG RAPLNQKEIQ QYNQILASQG LKAFIGAMVN GMEYLQTFGE DTVPYRRFPT LPAANFPNTE RLYNKLTKQD KELVVPSFT PVVKVGG |
-Macromolecule #5: Orange carotenoid-binding protein
Macromolecule | Name: Orange carotenoid-binding protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 / Kazusa |
Molecular weight | Theoretical: 34.684605 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPFTIDSARG IFPNTLAADV VPATIARFSQ LNAEDQLALI WFAYLEMGKT LTIAAPGAAS MQLAENALKE IQAMGPLQQT QAMCDLANR ADTPLCRTYA SWSPNIKLGF WYRLGELMEQ GFVAPIPAGY QLSANANAVL ATIQGLESGQ QITVLRNAVV D MGFTAGKD ...String: MPFTIDSARG IFPNTLAADV VPATIARFSQ LNAEDQLALI WFAYLEMGKT LTIAAPGAAS MQLAENALKE IQAMGPLQQT QAMCDLANR ADTPLCRTYA SWSPNIKLGF WYRLGELMEQ GFVAPIPAGY QLSANANAVL ATIQGLESGQ QITVLRNAVV D MGFTAGKD GKRIAEPVVP PQDTASRTKV SIEGVTNATV LNYMDNLNAN DFDTLIELFT SDGALQPPFQ RPIVGKENVL RF FREECQN LKLIPERGVT EPAEDGFTQI KVTGKVQTPW FGGNVGMNIA WRFLLNPEGK IFFVAIDLLA SPKELLNFAR |
-Macromolecule #6: Phycobilisome rod-core linker polypeptide CpcG
Macromolecule | Name: Phycobilisome rod-core linker polypeptide CpcG / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC 6803 / Kazusa |
Molecular weight | Theoretical: 28.938758 KDa |
Sequence | String: MALPLLNYAP KSQNVRVEGY EIGSEEKPVV FTTENILSSS DMDNLIEAAY RQIFFHAFKW DREKVLESQL RNGQITVRDF VRGLLLSNT FRNSFYEKNS NYRFVEHCVQ KILGRDVYSE REKIAWSIVV ATKGYQGLID DLLNSDEYLN NFGYDTVPYQ R RRNLPGRE ...String: MALPLLNYAP KSQNVRVEGY EIGSEEKPVV FTTENILSSS DMDNLIEAAY RQIFFHAFKW DREKVLESQL RNGQITVRDF VRGLLLSNT FRNSFYEKNS NYRFVEHCVQ KILGRDVYSE REKIAWSIVV ATKGYQGLID DLLNSDEYLN NFGYDTVPYQ R RRNLPGRE AGELPFNIKS PRYDAYHRRQ LGFPQIVWQN EVRRFIPQEK KLTAGNPMNF LGMARSINPA ANTIPKVSAQ NI NIEASVP RR |
-Macromolecule #7: PHYCOCYANOBILIN
Macromolecule | Name: PHYCOCYANOBILIN / type: ligand / ID: 7 / Number of copies: 24 / Formula: CYC |
---|---|
Molecular weight | Theoretical: 588.694 Da |
Chemical component information | ChemComp-CYC: |
-Macromolecule #8: beta,beta-carotene-4,4'-dione
Macromolecule | Name: beta,beta-carotene-4,4'-dione / type: ligand / ID: 8 / Number of copies: 2 / Formula: 45D |
---|---|
Molecular weight | Theoretical: 564.84 Da |
Chemical component information | ChemComp-45D: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.8 mg/mL |
---|---|
Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: GOLD / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV / Details: Manual blotting. |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | PDB-7scc: |